BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717090.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,818,468 number of mapped reads = 1,593,134 (87.61%) number of supplementary alignments = 23,629 (1.3%) number of secondary alignments = 0 number of mapped bases = 124,896,312 bp number of sequenced bases = 124,844,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,281 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5736 >>>>>>> ACTG content number of A's = 31,427,972 bp (25.17%) number of C's = 23,723,059 bp (19%) number of T's = 39,338,532 bp (31.51%) number of G's = 30,347,514 bp (24.31%) number of N's = 7,067 bp (0.01%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,061,126 number of insertions = 11,619 mapped reads with insertion percentage = 0.72% number of deletions = 29,966 mapped reads with deletion percentage = 1.85% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.4685X There is a 3.44% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9936369 0.039864971891083074 0.6804966771737189 chr2 243199373 11114222 0.04570004380726755 0.7173422438038092 chr3 198022430 8375560 0.04229601666841479 0.23526192685681088 chr4 191154276 8103543 0.04239268495359214 0.25793464855615866 chr5 180915260 7247876 0.040062270037364456 0.2359197106547177 chr6 171115067 7784335 0.04549181516552251 0.3170707111565452 chr7 159138663 7484738 0.047032806854736486 0.6165161355680818 chr8 146364022 6490640 0.04434587073591077 0.6359259547757145 chr9 141213431 5670864 0.040158106490592954 0.5308760799130704 chr10 135534747 6354136 0.04688197042194649 0.43775202320848333 chr11 135006516 5918581 0.04383922476749196 0.4625010364729005 chr12 133851895 5533815 0.0413428214819073 0.23976815496143164 chr13 115169878 3857243 0.033491769436449347 0.20586537146212164 chr14 107349540 3657291 0.034068995544834196 0.2982089370673545 chr15 102531392 3480205 0.03394282406699404 0.2145293697338214 chr16 90354753 3514598 0.038897765566355984 0.2800878207622335 chr17 81195210 3527686 0.0434469718102829 0.26680283001211264 chr18 78077248 3511620 0.04497622662110222 1.0743333662084902 chr19 59128983 2688051 0.04546080219238677 0.5411379655337778 chr20 63025520 2470985 0.03920610254385842 0.25677863108173515 chr21 48129895 2226195 0.046253892720937786 0.266993412757182 chr22 51304566 1632110 0.03181217827668594 0.20361018340243497 chrMT 16571 7483 0.45157202341439867 0.7912147247248245 chrX 155270560 4014594 0.025855474469854426 0.3138319815840061 chrY 59373566 293572 0.004944489943555016 0.14937598541264377